Rv0818 (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: two-component system OmpR family response regulator
- REFSEQ: transcriptional regulatory protein
- PATRIC: Phosphate regulon transcriptional regulatory protein PhoB (SphR)
- TUBERCULIST: Transcriptional regulatory protein
- NCBI: Transcriptional regulatory protein
- updated information (H37Rv4):
  - gene name: glnR
  - function: regulates nitrogen assimilation
  - reference: Liu (2018) PMID: 29988377; Williams (2015) PMID: 26077160
Type: Not Target
Start: 910972
End: 911739
Operon:

Trans-membrane region:
Role: I.J.2 - Two component systems
GO terms:
- GO:0045893 - positive regulation of transcription, DNA-templated (Uniprot)
- GO:0042128 - nitrate assimilation (Uniprot)
- GO:0019217 - regulation of fatty acid metabolic process (Uniprot)
- GO:0010468 - regulation of gene expression (Uniprot)
- GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
- GO:0006351 - transcription, DNA-templated (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005622 - intracellular (Uniprot)
- GO:0003677 - DNA binding (Uniprot)
- GO:0000160 - phosphorelay signal transduction system (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
Orthologs among selected mycobacteria
Protein structure:
Search for Homologs in PDB

Top 10 Homologs in PDB (as of Nov 2020):

PDB	aa ident	species	PDB title
4O1I	99%	Mycobacterium tuberculosis	Crystal Structure of the regulatory domain of MtbGlnR
4O1H	56%	Amycolatopsis mediterranei	Crystal Structure of the regulatory domain of AmeGlnR
6CQG	52%	Streptococcus pneumoniae	YycF Effector Domain Structure without DNA bound
5ZA3	50%	Streptococcus mutans	Structure of a C-terminal S. mutans response regulator VicR domain
2HWV	50%	Enterococcus faecalis	Crystal structure of an essential response regulator DNA binding domain, VicRc in Enterococcus faecalis, a member of the YycF subfamily.
2D1V	48%	Bacillus subtilis	Crystal structure of DNA-binding domain of Bacillus subtilis YycF
2ZXJ	47%	Staphylococcus aureus	Crystal structure of YycF DNA-binding domain from Staphylococcus aureus
4IXA	40%	Staphylococcus epidermidis	Structure of DNA-binding domain of the response regulator SaeR from Staphylococcus epidermidis
5U8M	39%	Streptococcus pneumoniae (strain Hungary19A-6)	A novel family of redox sensors in the streptococci evolved from two-component response regulators
2MLK	39%	Klebsiella pneumoniae	Three-dimensional structure of the C-terminal DNA-binding domain of RstA protein from Klebsiella pneumoniae

Links to additional information on Rv0818:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -0.314 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

LLELLLLTSELYPDPVLPALSLLPHTVRTAPAEASSLLEAGNADAVLVDARNDLSSGRGLCRLLSSTGRSIPVLAVVSEGGLVAVSADWGLDEILLLSTG
PAEIDARLRLVVGRRGDLADQESLGKVSLGELVIDEGTYTARLRGRPLDLTYKEFELLKYLAQHAGRVFTRAQLLHEVWGYDFFGGTRTVDVHVRRLRAK
LGPEHEALIGTVRNVGYKAVRPARGRPPAADPDDEDADPGRDGMQEPLVDPLRSQ

(Nucleotide sequence available on KEGG)

Additional Information

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across >100 conditions *new*

Classification	Condition	Strain	Method	Reference	Notes
Non-Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 11 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 11 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 11 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 11 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 11 sites
Non-Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Non-Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 1.53
Growth-Advantage	7H09/7H10 + rich media	H37RvMA	MotifHMM	DeJesus et al. (2017)	Fully saturated (14 reps).

TnSeq Data No data currently available.

No TnSeq data currently available for this Target.

RNASeq Data No data currently available.

No RNA-Seq data currently available for this Target.

Metabolomic Profiles No data currently available.

No Metabolomic data currently available for this Target.

Proteomic Data No data currently available.

No Proteomic data currently available for this Target.

Regulatory Relationships from Systems Biology

BioCyc

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

NOTE: Green edges represent the connected genes being classified as differentially essential as a result of the middle gene being knocked out. These interactions are inferred based on RNASeq.

Interactions based on ChIPSeq data

RNA processing and modification

Energy production and conversion

Chromatin structure and dynamics

Amino acid transport and metabolism

Cell cycle control, cell division, chromosome partitioning

Carbohydrate transport and metabolism

Nucleotide transport and metabolism

Lipid transport and metabolism

Coenzyme transport and metabolism

Transcription

Translation, ribosomal structure and biogenesis

Cell wall/membrane/envelope biogenesis

Replication, recombination and repair

Posttranslational modification, protein turnover, chaperones

Cell motility

Secondary metabolites biosynthesis, transport and catabolism

Inorganic ion transport and metabolism

Function unknown

General function prediction only

Intracellular trafficking, secretion, and vesicular transport

Signal transduction mechanisms

Extracellular structures

Defense mechanisms

Nuclear structure

Cytoskeleton

BioCyc Co-regulated genes based on gene expression profiling (Systems Biology, Inferelator Network)

Differentially expressed as result of RNASeq in glycerol environment (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

Conditionally essential as result of TNSeq (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

BioCyc Transcription factor binding based on ChIP-Seq (Systems Biology)

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- Rv0045c (-) (Direct binding)
- Rv0244c (fadE5) (Direct binding)
- Rv0245 (-) (Direct binding)
- Rv0252 (nirB) (Direct binding)
- Rv0469 (umaA) (Direct binding)
- Rv0501 (galE2) (Direct binding)
- Rv1322A (-) (Direct binding)
- Rv1386 (PE15) (Direct binding)
- Rv1542c (glbN) (Direct binding)
- Rv1791 (PE19) (Direct binding)
- Rv2281 (pitB) (Direct binding)
- Rv3229c (desA3) (Direct binding)
- Rv3384c (vapC46) (Direct binding)
- Rv3385c (vapB46) (Direct binding)
- Rv3386 (-) (Direct binding)
- Rv0044c (-) (Upstream of operon)
- Rv0253 (nirD) (Upstream of operon)
- Rv0502 (-) (Upstream of operon)
- Rv1387 (PPE20) (Upstream of operon)
- Rv3387 (-) (Upstream of operon)
Bound By:
- No bindings to other targets were found.

Property	Value	Creator	Evidence	PMID	Comment
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3544c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3545c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3250c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3251c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3252c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3543c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv1464	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv1465	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv1466	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3249c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv1460	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv1461	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv1462	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv1463	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

TB Genome Annotation Portal

Rv0818 (-)

Amino Acid Sequence

Additional Information

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

Interactions based on ChIPSeq data

Interactions based on ChIPSeq data (Minch et al. 2014)

Interactions based on TFOE data (Rustad et al. 2014)

TBCAP

Comments